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Wang X, Yang S, Yang G, Lin J, Zhao P, Ding J, Sun H, Meng T, Yang MM, Kang L, Liang Z. Novel risk score model for non-proliferative diabetic retinopathy based on untargeted metabolomics of venous blood. Front Endocrinol (Lausanne) 2023; 14:1180415. [PMID: 37670880 PMCID: PMC10476524 DOI: 10.3389/fendo.2023.1180415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023] Open
Abstract
Background and Purpose Nonproliferative diabetic retinopathy (NPDR) occurs in the early stages of Diabetic retinopathy (DR), and the study of its metabolic markers will help to prevent DR. Hence, we aimed to establish a risk score based on multiple metabolites through untargeted metabolomic analysis of venous blood from NPDR patients and diabetic non-DR patients. Experimental Approach Untargeted metabolomics of venous blood samples from patients with NPDR, diabetes melitus without DR were performed using high-performance liquid chromatography-mass spectrometry. Results Detailed metabolomic evaluation showed distinct clusters of metabolites in plasma samples from patients with NPDR and diabetic non-DR patients. NPDR patients had significantly higher levels of phenylacetylglycine, L-aspartic acid, tiglylglycine, and 3-sulfinato-L-alaninate, and lower level of indolelactic acid, threonic acid, L-arginine (Arg), and 4-dodecylbenzenesulfonic acid compared to control. The expression profiles of these eight NPDR risk-related characteristic metabolites were analyzed using Cox regression to establish a risk score model. Subsequently, univariate and multivariate Cox regression analyses were used to determine that this risk score model was a predictor of independent prognosis for NPDR. Conclusions Untargeted metabolome analysis of blood metabolites revealed unreported metabolic alterations in NPDR patients compared with those in diabetic non-DR patients or MH. In the venous blood, we identified depleted metabolites thA and Arg, indicating that they might play a role in NPDR development.
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Affiliation(s)
- Xinyu Wang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
- Department of Nephrology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shu Yang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China
- The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Guangyan Yang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China
- The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Jialong Lin
- Department of Cardiovascular Medicine, The Fourth Affiliated Hospital of Guangzhou Medical University, Zengcheng District People’s Hospital of Guangzhou, Guangzhou, China
| | - Pengfei Zhao
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jingyun Ding
- Department of Geriatric, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongyan Sun
- Department of Ophthalmology, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Ting Meng
- Department of Ophthalmology, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Ming Ming Yang
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China
- The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Department of Ophthalmology, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lin Kang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China
- The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- The Biobank of National Innovation Center for Advanced Medical Devices, Shenzhen People’s Hospital, Shenzhen, China
| | - Zhen Liang
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China
- The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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Li Y(J, Kresock E, Kuplicki R, Savitz J, McKinney BA. Differential expression of MDGA1 in major depressive disorder. Brain Behav Immun Health 2022; 26:100534. [PMID: 36247836 PMCID: PMC9563614 DOI: 10.1016/j.bbih.2022.100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/08/2022] [Accepted: 10/09/2022] [Indexed: 11/09/2022] Open
Abstract
The identification of gene expression-based biomarkers for major depressive disorder (MDD) continues to be an important challenge. In order to identify candidate biomarkers and mechanisms, we apply statistical and machine learning feature selection to an RNA-Seq gene expression dataset of 78 unmedicated individuals with MDD and 79 healthy controls. We identify 49 genes by LASSO penalized logistic regression and 45 genes at the false discovery rate threshold 0.188. The MDGA1 gene has the lowest P-value (4.9e-5) and is expressed in the developing brain, involved in axon guidance, and associated with related mood disorders in previous studies of bipolar disorder (BD) and schizophrenia (SCZ). The expression of MDGA1 is associated with age and sex, but its association with MDD remains significant when adjusted for covariates. MDGA1 is in a co-expression cluster with another top gene, ATXN7L2 (ataxin 7 like 2), which was associated with MDD in a recent GWAS. The LASSO classification model of MDD includes MDGA1, and the model has a cross-validation accuracy of 79%. Another noteworthy top gene, IRF2BPL, is in a close co-expression cluster with MDGA1 and may be related to microglial inflammatory states in MDD. Future exploration of MDGA1 and its gene interactions may provide insights into mechanisms and heterogeneity of MDD. We use penalized regression to select differentially expressed genes and characterize their relationships through clustering. We identify MDGA1 as the most differentially expressed gene between MDD and healthy controls using RNA-Seq. Previous studies have implicated MDGA1 in psychiatric disorders, such as schizophrenia and bipolar disorder, but not in MDD. Different psychiatric disorders have some genetic associations in common due to shared neural pathways between disorders. A top gene, IRF2BPL, in a close co-expression cluster with MDGA1 may be related to microglial inflammatory states in MDD. Future investigation of interactions of MDGA1 and IRF2BPL may provide insights into mechanisms and heterogeneity of MDD.
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Dawkins BA, Garman L, Cejda N, Pezant N, Rasmussen A, Rybicki BA, Levin AM, Benchek P, Seshadri C, Mayanja-Kizza H, Iannuzzi MC, Stein CM, Montgomery CG. Novel HLA associations with outcomes of Mycobacterium tuberculosis exposure and sarcoidosis in individuals of African ancestry using nearest-neighbor feature selection. Genet Epidemiol 2022; 46:463-474. [PMID: 35702824 DOI: 10.1002/gepi.22490] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/07/2022]
Abstract
Tuberculosis and sarcoidosis are inflammatory diseases characterized by granulomas that may occur in any organ but are often found in the lung. The panoply of classical human leukocyte antigen (HLA) alleles associated with occurrence and/or severity of both diseases varies considerably across studies. This heterogeneity of results, due to variation in factors like ancestry and disease subphenotype, as well as the use of simple modeling strategies to elucidate likely complex relationships, has made conclusions about underlying commonalities difficult. Here we perform HLA association analyses in individuals of African ancestry, using a greater resolution to include subphenotypes of disease and employing more comprehensive analytical techniques. Using a novel application of nearest-neighbor feature selection to score allelic importance, we investigated HLA allele association with Mycobacterium tuberculosis exposure outcomes in the first analysis of both latent Mycobacterium tuberculosis infection and active disease compared with those who, despite long-term exposure to active index cases, have neither positive diagnostic tests nor display clinical symptoms. We also compared persistent to resolved sarcoidosis. This led to the identification of novel HLA associations and evidence of main effects and interaction effects. We found strikingly similar main effects and interaction effects at HLA-DRB1, -DQB1, and -DPB1 in those resistant to tuberculosis (either latent or active) and persistent sarcoidosis.
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Affiliation(s)
- Bryan A Dawkins
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Lori Garman
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Nicholas Cejda
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Nathan Pezant
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA.,Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan, USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Michael C Iannuzzi
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Courtney G Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
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Dawkins BA, Le TT, McKinney BA. Theoretical properties of distance distributions and novel metrics for nearest-neighbor feature selection. PLoS One 2021; 16:e0246761. [PMID: 33556091 PMCID: PMC7870093 DOI: 10.1371/journal.pone.0246761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/25/2021] [Indexed: 11/18/2022] Open
Abstract
The performance of nearest-neighbor feature selection and prediction methods depends on the metric for computing neighborhoods and the distribution properties of the underlying data. Recent work to improve nearest-neighbor feature selection algorithms has focused on new neighborhood estimation methods and distance metrics. However, little attention has been given to the distributional properties of pairwise distances as a function of the metric or data type. Thus, we derive general analytical expressions for the mean and variance of pairwise distances for Lq metrics for normal and uniform random data with p attributes and m instances. The distribution moment formulas and detailed derivations provide a resource for understanding the distance properties for metrics and data types commonly used with nearest-neighbor methods, and the derivations provide the starting point for the following novel results. We use extreme value theory to derive the mean and variance for metrics that are normalized by the range of each attribute (difference of max and min). We derive analytical formulas for a new metric for genetic variants, which are categorical variables that occur in genome-wide association studies (GWAS). The genetic distance distributions account for minor allele frequency and the transition/transversion ratio. We introduce a new metric for resting-state functional MRI data (rs-fMRI) and derive its distance distribution properties. This metric is applicable to correlation-based predictors derived from time-series data. The analytical means and variances are in strong agreement with simulation results. We also use simulations to explore the sensitivity of the expected means and variances in the presence of correlation and interactions in the data. These analytical results and new metrics can be used to inform the optimization of nearest neighbor methods for a broad range of studies, including gene expression, GWAS, and fMRI data.
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Affiliation(s)
- Bryan A Dawkins
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Trang T Le
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Brett A McKinney
- Department of Mathematics, University of Tulsa, Tulsa, OK, United States of America.,Tandy School of Computer Science, University of Tulsa, Tulsa, OK, United States of America
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Arabnejad M, Montgomery CG, Gaffney PM, McKinney BA. Nearest-Neighbor Projected Distance Regression for Epistasis Detection in GWAS With Population Structure Correction. Front Genet 2020; 11:784. [PMID: 32774345 PMCID: PMC7387719 DOI: 10.3389/fgene.2020.00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/01/2020] [Indexed: 11/24/2022] Open
Abstract
Nearest-neighbor Projected-Distance Regression (NPDR) is a feature selection technique that uses nearest-neighbors in high dimensional data to detect complex multivariate effects including epistasis. NPDR uses a regression formalism that allows statistical significance testing and efficient control for multiple testing. In addition, the regression formalism provides a mechanism for NPDR to adjust for population structure, which we apply to a GWAS of systemic lupus erythematosus (SLE). We also test NPDR on benchmark simulated genetic variant data with epistatic effects, main effects, imbalanced data for case-control design and continuous outcomes. NPDR identifies potential interactions in an epistasis network that influences the SLE disorder.
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Affiliation(s)
- Marziyeh Arabnejad
- Tandy School of Computer Science, University of Tulsa, Tulsa, OK, United States
| | - Courtney G Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Brett A McKinney
- Tandy School of Computer Science, University of Tulsa, Tulsa, OK, United States.,Department of Mathematics, University of Tulsa, Tulsa, OK, United States
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